Software
The BDTNP is providing software developed to process, visualize and analyze 3D gene expression data.
- PointCloudXplore: Visualization and analysis of the data in PointCloud and Virtual Embryo Files.
- PointCloudToolBox:
Image analysis methods to generate PointCloud files that contain geometric data for each nucleus (position, volume, etc.),
and the measured levels of gene expression in a single embryo.
- PointCloudAlign:
Registration methods to place gene expression data from many embryos into a VirtualEmbryo file,
to allow comparison between the expression patterns of more than two or three genes.
-
Nonparametric Identification of Regulatory Interactions (NODE):
A method that determines the correlation between transcription factor protein concentrations
and temporal changes in the mRNA expression of putative target genes for small clusters of cells
throughout the embryo.
- Biological Imaging Database (BID):
A relational database, and web-based user interface, for tracking 3D gene expression experiments.
The source code and instructions are available upon request.
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